[gmx-users] Re: System equilibrium problems

Parker de Waal Parker.deWaal09 at kzoo.edu
Fri Jun 14 16:45:58 CEST 2013

HI Maggin,

The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of

I'm currently looking into the rvdw value as you suggested as well as the
fourierspacing as Mark suggested.

However to help with this problem I've uploaded all of .mdp files as well
as my bash script here ->
Maybe there is a problem with my choice of box size? -bt cubic -d 1?
Viewing the boxed and solvated system showed a distance of ~10A between the
protein and the box which should be ample.

Additionally a full output log of the run can be found here ->
which seems to be error free until the final md run.

Thanks Everyone,

On Fri, Jun 14, 2013 at 9:56 AM, maggin <maggin.chen at gmail.com> wrote:

> Hi, Parker,
> gromos53a6 force field,  rvdw=1,  if it right ? please check.
> Your ref_p = 1.0, So, Pressure average of 1.9 is come from which step? NVT,
> NPT, md ?
> Actually, we use:  g_energy -f npt.edr -o pressure.xvg
> to see if NPT has reached equilibrium.
> g_energy -f nvt.edr
> to see if NVT has reached equilibrium.
> maggin
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/System-equilibrium-problems-tp5009137p5009157.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list